Wafer-level performance prediction techniques have been increasingly gaining attention in production LSI testing due to their ability to reduce measurement costs without compromising test quality. Despite the availability of several efficient methods, the site-to-site variation commonly observed in multi-site testing for radio frequency circuits remains inadequately addressed. In this manuscript, we propose a wafer-level performance prediction approach for multi-site testing that takes into account the site-to-site variation. Our proposed method is built on the Gaussian process, a widely utilized wafer-level spatial correlation modeling technique, and enhances prediction accuracy by extending hierarchical modeling to leverage the test site information test engineers provide. Additionally, we propose a test-site sampling method that maximizes cost reduction while maintaining sufficient estimation accuracy. Our experimental results, which employ industrial production test data, demonstrate that our proposed method can decrease the estimation error to 1/19 of that a conventional method achieves. Furthermore, our sampling method can reduce the required measurements by 97% while ensuring satisfactory estimation accuracy.